USDA-ARS Western Regional Research Center, Albany, CA 94710, USA.
BMC Genomics. 2010 Oct 25;11:600. doi: 10.1186/1471-2164-11-600.
Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families.
We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, the Brachypodium and sorghum proteins generally cluster with those from other monocots.
This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a grass model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.
糖苷水解酶裂解碳水化合物与另一种碳水化合物、蛋白质、脂质或其他部分之间的键。编码糖苷水解酶的基因存在于从古菌到动物的广泛生物体中，并且在植物基因组中相对丰富。在植物中，这些酶参与多种过程，包括淀粉代谢、防御和细胞壁重塑。糖苷水解酶基因已在水稻（模型双子叶植物拟南芥和快速生长的杨树（杨树）中进行了编目。为了提高我们对植物中糖苷水解酶的一般理解，特别是对禾本科植物的理解，我们注释了禾本科植物短柄草（新兴的单子叶模式植物）和高粱中的糖苷水解酶基因。然后，我们在整个基因组和单个糖苷水解酶家族的水平上比较了不同物种的糖苷水解酶。
我们在短柄草中鉴定出 356 个糖苷水解酶基因，在高粱中鉴定出 404 个糖苷水解酶基因。相应的蛋白质分为 34 个相同的家族，这些家族在水稻、拟南芥和杨树中都有代表，有助于定义一个可能在开花植物中普遍存在的糖苷水解酶家族图谱。对于几个糖苷水解酶家族（GH5、GH13、GH18、GH19、GH28 和 GH51），我们一起呈现了详细的文献综述，并检查了家族结构。对个别家族的分析揭示了单子叶植物和双子叶植物以及物种之间的相似之处和区别。共享的进化历史似乎被谱系特异性的扩张或缺失所改变。在 GH 家族中，短柄草和高粱蛋白通常与其他单子叶植物的蛋白聚类。
这项工作为进一步比较和功能分析植物糖苷水解酶奠定了基础。定义短柄草糖苷水解酶为研究这些酶及其在植物中的多种作用的禾本科模式奠定了基础。从短柄草获得的见解将为转化研究提供信息，为提高谷类作物和生物能源草的应用提供信息。
